Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation...
It is necessary to detect highly variable regions in envelopes of viruses as it allows the establishment of the viruses in the human body. A new...
GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of...
This is a basic tutorial on removing the hetero-atoms (HETATMS) and chains from PDB files. It is an essential step for computational and molecular dynamics simulation.
In this tutorial, we are performing MD simulation in mixed solvents of methanol and water using GROMACS [1,2]. You can follow our previous articles for MD...
In this article, we summarize the main findings made in bioinformatics this month.
Clustal packages [1,2] are quite useful in multiple sequence alignments. Especially, when you need specific outputs from the command-line. In this article, we will install CustalW2...
This is a continuation article of our previous post: Tutorial-I: Functional Divergence Analysis using DIVERGE 3.0 software. In our last tutorial, we explained Type-II functional divergence....
DIVERGE is a tool to detect functional divergence between member genes of a protein family based on (site-specific) shifted evolutionary rates after gene duplication or speciation...
A new webserver called DISTEVAL [1] is developed that evaluates the predicted protein distances. This web server evaluates the inter-residue distances and offers several other features...